Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, United Kingdom.
Proc Natl Acad Sci U S A. 2013 Jan 8;110(2):E132-40. doi: 10.1073/pnas.1213624110. Epub 2012 Dec 19.
A question of fundamental importance concerning protein folding in vivo is whether the kinetics of translation or the thermodynamics of the ribosome nascent chain (RNC) complex is the major determinant of cotranslational folding behavior. This is because translation rates can reduce the probability of cotranslational folding below that associated with arrested ribosomes, whose behavior is determined by the equilibrium thermodynamics of the RNC complex. Here, we combine a chemical kinetic equation with genomic and proteomic data to predict domain folding probabilities as a function of nascent chain length for Escherichia coli cytosolic proteins synthesized on both arrested and continuously translating ribosomes. Our results indicate that, at in vivo translation rates, about one-third of the Escherichia coli cytosolic proteins exhibit cotranslational folding, with at least one domain in each of these proteins folding into its stable native structure before the full-length protein is released from the ribosome. The majority of these cotranslational folding domains are influenced by translation kinetics which reduces their probability of cotranslational folding and consequently increases the nascent chain length at which they fold into their native structures. For about 20% of all cytosolic proteins this delay in folding can exceed the length of the completely synthesized protein, causing one or more of their domains to switch from co- to posttranslational folding solely as a result of the in vivo translation rates. These kinetic effects arise from the difference in time scales of folding and amino-acid addition, and they represent a source of metastability in Escherichia coli's proteome.
关于体内蛋白质折叠的一个基本问题是，翻译的速度还是核糖体新生链（RNC）复合物的热力学是共翻译折叠行为的主要决定因素。这是因为翻译速度可以降低共翻译折叠的概率，使其低于与被阻止的核糖体相关的概率，而核糖体的行为是由 RNC 复合物的平衡热力学决定的。在这里，我们将化学动力学方程与基因组和蛋白质组数据相结合，预测大肠杆菌细胞质蛋白在被阻止的和连续翻译的核糖体上合成时，作为新生链长度的函数的结构域折叠概率。我们的结果表明，在体内翻译速度下，大约三分之一的大肠杆菌细胞质蛋白表现出共翻译折叠，在这些蛋白质中的每一个中，至少有一个结构域在从核糖体上释放全长蛋白质之前折叠成其稳定的天然结构。这些共翻译折叠结构域中的大多数受到翻译动力学的影响，降低了它们共翻译折叠的概率，从而增加了它们折叠成天然结构的新生链长度。对于所有细胞质蛋白的约 20%，这种折叠的延迟可以超过完全合成蛋白质的长度，导致它们的一个或多个结构域仅由于体内翻译速度而从共翻译折叠切换到翻译后折叠。这些动力学效应源于折叠和氨基酸添加的时间尺度的差异，它们代表了大肠杆菌蛋白质组中一种亚稳性的来源。
